title: RNAseq in Arabidopsis prefoldin mutants

status: Public on Dec 22 2020

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

summary: This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants

overall_design: 12 biological samples from 4 different conditions and genotype, including the Col-0 WT in each condition

first: Noel

last: Blanco-Touriñán

first: David

last: Esteve-Bruna

first: Antonio

last: Serrano-Mislata

first: Rosa

last: Esquinas-Ariza

first: Cristian

last: Carrasco-López

first: Claudio

last: Novella-Rausell

first: Alberto

last: Palacios-Abella

first: Pedro

last: Carrasco

first: Julio

last: Salinas

first: Miguel

last: Blázquez

last: Alabadí

first: Francesca

last: Resentini

first: Cristina

last: Úrbez


title: CRAC of Nab3 in yeast cells accumulating a circular RNA containing Nab3 binding sites (the decoy) or an empty control

status: Public on Jan 12 2021

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the analysis of in vivo, genomewide binding of Nab3  under conditions in which non-degradable targets of Nab3 accumulate. We aimed at mimicking the effect of defective degradation of non-coding RNAs (Cryptic Unstable Transcripts, CUT) that can be bound by Nab3 on the co-transcriptional recruitment of Nab3 for transcription termination.

overall_design: The RNA was crosslinked to Nab3 by exposing the cells to UV irradiation and sequenced after purification of  HTP-tagged Nab3 under stringent and denaturing conditions. This reveals the extent of binding of Nab3 to its different targets . Circular RNAs were generated by preventing debranching and subsequent degradation of an intron lariat containing a CUT in a strain deleted for the debranching enzyme Dbr1 as described in  Villa, T., Barucco, M., Martin-Niclos, M.-J., Jacquier, A. & Libri, D. Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Reports 32, 107942 (2020).

first: Tommaso

last: Villa


title: Neuronal activity promotes nuclear proteasome-mediated degradation of PDCD4 to regulate activity-dependent transcription in neurons

status: Public on Dec 15 2020

city: Los Angeles

first: Kelsey

last: Martin

state: CA

address: 615 Charles E Young Drive South

department: Biological Chemistry

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Activity-dependent gene expression is critical for synapse development and plasticity. To elucidate novel mechanisms linking neuronal activity to changes in transcription, we compared the nuclear proteomes of tetrodotoxin-silenced and bicuculline-stimulated cultured neurons using nuclear-localized APEX2 proximity biotinylation and mass spectrometry. The tumor suppressor protein PDCD4 was enriched in the nuclear proteome of silenced neurons, and PDCD4 levels rapidly decreased in the nucleus and cytoplasm of stimulated neurons. The activity-dependent decrease of PDCD4 was prevented by inhibitors of both PKC and proteasome activity and by a phospho-incompetent mutation of Ser71 in the βTRCP ubiquitin ligase-binding motif of PDCD4. We compared the activity-dependent transcriptomes of neurons expressing wildtype or degradation-resistant (S71A) PDCD4. We identified 91 genes as PDCD4 targets at the transcriptional level, including genes encoding proteins critical for synapse formation, remodeling, and transmission. Our findings indicate that regulated degradation of nuclear PDCD4 facilitates activity-dependent transcription in neurons.

overall_design: DIV 20 rat forebrain culture mRNA profiles, neurons transduced with either WT or S71A PDCD4, neurons were silenced (TTX) or stimulated (BIC) for 1 hr, cultures treated with vehicle or cycloheximide, 3 biological replicates each condition (24 samples total)

first: Wendy

middle: A

last: Herbst

first: Weixian

last: Deng

first: James

last: Wohlschlegel

first: Jennifer

middle: M

last: Achiro

middle: C


title: Clinical, histopathologic and molecular features of idiopathic and diabetic nodular mesangial sclerosis in humans

status: Public on Dec 09 2020

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Idiopathic nodular mesangial sclerosis, also called idiopathic nodular glomerulosclerosis (ING) is a rare clinical entity with unclear pathogenesis. The hallmark of this disease is the presence of nodular mesangial sclerosis on histology without clinical evidence of diabetes mellitus or other predisposing diagnoses. To achieve insights into its pathogenesis, we queried the clinical, histopathologic and transcriptomic features of ING and nodular diabetic nephropathy (DN)

overall_design: Cross-sectional human kidney biopsies or nephrectomies embedded in OCT underwent laser microdissection of glomeruli and RNA was sequenced.

first: Eadon

last: Michael

first: Ricardo

last: Ferreira


title: RNA-seq, ATAC-seq and Hi-C profiles of B cells and naïve and activated T cells from human peripheral blood

status: Public on Jan 21 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days to induce activation. The B cells and naive and activated T cells were profiled by RNA-seq, ATAC-seq and Hi-C.

overall_design: Cells were isolated from two human donors, resulting in two biological replicates of each combination of cell type and activation status.

first: Naiara

middle: G

last: Bediaga

first: Alexandra

last: Garnham

first: Hannah

last: Coughlan


title: Transcriptomic profiling of MDA-MB-231 cells treated with cytostatic compounds

status: Public on Dec 12 2020

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: Transcriptomic profiling of MDA-MB-231 cells treated with Paclitaxel , 4-ethyl-N-(7-hydroxy-3,4-dihydroisoquinolin-2-(1H)-yl)benzamide (GM-453) or LDHAB inhibitor   (6R)-3-[(2-Chlorophenyl)thio]-5,6-dihydro-4-hydroxy-6-[4-(4-morpholinyl)phenyl]-6-(3-thienyl)-2(1H)-pyridinone, (R)-3-(2-Chlorophenyl)sulfanyl-6-(4-morpholinophenyl)-6-(3-thienyl)piperidine-2,4-dione (GNE-140)

overall_design: The effects of  cytostatic compounds paclitaxel , 4-ethyl-N-(7-hydroxy-3,4-dihydroisoquinolin-2-(1H)-yl)benzamide (GM-453)  and GNE-140 (an LDHAB inhibitor) were evaluated for effects on the whole transcriptome: including mRNAs and long intergenic non-coding RNA transcripts using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc.

first: Madhavi

last: Gangapuram

first: Kinfe

last: Redda

first: Karam

last: Soliman


title: Chromatin profiling of CLL cells with hyperactivated Notch1 compared to control CLL cells [ATAC-seq]

status: Public on Dec 19 2020

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: NOTCH1 gain-of-function mutations are recurrent in B cell chronic lymphocytic leukemia (B-CLL), where they are associated with accelerated disease progression and refractoriness to chemotherapy. The specific role of NOTCH1 in the development and progression of this malignancy is unclear. Herein we assess the impact of loss of Notch signaling and pathway hyperactivation in an in vivo mouse model of CLL (IgH.TEm) that faithfully recapitulates many features of the human pathology. Ablation of canonical Notch signaling using conditional gene inactivation of RBP-J in immature hematopoietic or B cell progenitors delayed CLL induction and reduced incidence of mice developing disease.  In contrast, forced expression of a dominant active form of Notch resulted in more animals developing CLL with early disease onset. Comparative analysis of gene expression and epigenetic features of Notch gain-of-function and control CLL cells revealed direct and indirect regulation of cell cycle-associated genes, which led to increased proliferation of Notch gain-of-function CLL cells in vivo. These results demonstrate that Notch signaling facilitates disease initiation and promotes CLL cell proliferation and disease progression.

overall_design: ATAC chromatin profile comparisons of sorted CLL spenocytes (CD19+B220-) derived from IgH.TEμ;RNICΔ/+ mb1-Cre and  IgH.TEμ;RNIC+/+ mb1-Cre mice

first: Delphine

last: Tardivon

last: Zangger

first: Freddy

last: Radtke


title: Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

status: Public on Dec 08 2020

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

summary: Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, aptly named Small RNA in Haloferax Oxidative Stress (SHOxi). We demonstrated that SHOxi is a functional non-coding RNA that plays gene regulatory roles in the oxidative stress response of an extremophilic archaeon. We found that SHOxi likely regulates redox homeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. The decrease in the NAD+/NADH ratio resulting from the direct RNA-RNA interaction between SHOxi and its trans-target is instrumental in the survival of H. volcanii. The regulatory effects of SHOxi provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.

overall_design: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) and H98 (Δpyre2, ΔthyH) were used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC) or selection medium (Hv-Cab), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737) (Dyall-Smith, 2009). Uracil, tryptophan, thymidine, and hypoxanthine were added to a final concentration of 50 µg/mL, each. H. volcanii liquid cultures were exposed to H2O2 as previously described (Gelsinger & DiRuggiero, 2018b). In brief, cultures were grown in 160 mL of Hv-YPC or Hv-Cab under optimal conditions to an OD of 0.4 (mid exponential phase). 2 mM H2O2 was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 5,000 x g for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 6,000 x g for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction.  Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe were used to break down the cell pellet after addition of RNA lysis buffer to the frozen pellets to insure complete cell lysis. Total RNA was then extracted following the standard kit protocol. Total RNA was DNase I (NEB) treated (37 °C for 2 hours) as previously described (ref). Total RNA was then rRNA-depleted using the Ribo-zero Bacteria kit (Illumina). Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and either paired-end sequenced (2 x 150 bp) or single-end sequenced (100 bp) on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF). We used a read count-based differential expression analysis to identify putative targets of SHOxi that were differentially expressed during oxidative stress and in ΔSHOxi. The program featureCounts was used to rapidly count reads that map to the NCBI H. volcanii annotation. featureCounts was run with strand-specific options on, paired-end mode on or off, multi-mapping off. The read counts were then used in the R differential expression software package DESeq2 (ref). Briefly, read counts were converted into a data matrix and normalized by sequencing depth and geometric mean. Differential expression was calculated by finding the difference in read counts between the SHOxi knockout oxidative stress state to the normalized read counts from the wild-type oxidative stress normalized read counts. The differentially expressed mRNAs were filtered based on the statistical parameter of False Discovery Rate (FDR) under 5%. In addition, only mRNAs with converse differential expression levels (FDR < 5%) in our previous wild type no challenge/oxi stress differential expression comparison (Gelsinger & DiRuggiero, 2018b) were labeled as specific putative targets of SHOxi.

middle: R

first: Rahul

last: Reddy

first: Kathleen

last: Whittington

first: Sara

last: Debic

first: Jocelyne

last: DiRuggiero


title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

status: Public on Jan 18 2021

city: Davis

first: Alex

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

summary: Sequencing studies of autism spectrum disorder (ASD) cases have revealed a causal role for mutations to chromatin remodeling genes. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with one of the highest de novo mutation rates in sporadic ASD. However, the relationship between CHD8 genomic function and autism-relevant biology remains poorly elucidated. CHD8 binding studies have relied on Chromatin Immunoprecipitation followed by sequencing (ChIP-seq), but these datasets exhibit significant variation. ChIP-seq has technical limitations in the context of weak or indirect protein-DNA interactions or when high-performance antibodies are unavailable. Thus, complementary approaches are needed to establish CHD8 genomic targets. Here we used Targeted DamID in utero to characterize CHD8 binding activity in the developing embryonic mouse cortex. CHD8 Targeted DamID followed by sequencing (CHD8 TaDa-seq) revealed binding at previously identified genomic targets as well as at genes sensitive to Chd8 haploinsufficiency. CHD8 TaDa-seq showed greater sensitivity for CHD8 binding near a subset of genes specific to brain development and neuron function. These studies establish TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provide insights into the relationship between chromatin remodeling by CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.

overall_design: Targeted DamID sequencing of CHD8 binding loci via in utero electroporation of E17.5 mouse cortex.

first: A

last: Wade

first: Jelle

last: van den Ameele

first: Seth

middle: W

last: Cheetham

first: Rebecca

last: Yakob

first: Andrea

middle: H

last: Brand

middle: S


title: Expression of transcriptome analysis of human fabry kidney organoid

status: Public on Jan 16 2021

city: Seoul

first: Hae Jin

last: Cho

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: Catholic university

summary: Kidney organoids in vitro model enabled identification of a novel mechanism that may be used for the treatment of Fabry disease.

overall_design: Human inducible pluripotent stem cell line (CMC11) was obtained from the Catholic university of korea and maintained in mTesr1 medium. Total RNA was prepared from the kidney organoids and fabry kidney organoids using TRIzol (Invitrogen). Gene expression studies were performed using the Affymetrix One Cycle labeling kit. The data were summarized and normalized using the robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT). The results with gene level RMA analysis were exported and DEG analysis was performed. Statistical significance of the expression data was determined using LPE test and fold change in which the null hypothesis was that no difference exists among groups.

first: Yong

last: Kim

first: Jin


title: Gene expression profiling of CLL cells with hyperactivated Notch1 compared to control CLL cells [RNA-seq]

first: Nadine

last: Fournier

overall_design: Expression profile comparisons of sorted CLL spenocytes (CD19+B220-) derived from IgH.TEμ;RNIC lox/+ mb1-Cre, IgH.TEμ;RNIC lox/+ CD19-Cre  and  IgH.TEμ;RNIC lox/+ mice

last: Harduin


title: Screening RIPK3 dependent signaling pathway and genes expression in intestinal GVHD mice models

status: Public on Jan 28 2021

city: Suzhou

first: xiaoliang

last: yu

state: Jiangsu

address: Chongwen Road

country: China

institute: Suzhou Institute of Systems Medicine

summary: Lethally irradiated recipient C57BL/6 WT, RIPK3-/- and Villin-cre RIPK3fl/fl mice received Balb/c bone marrow and CD4+ T cells. After 17 days, total RNA was extracted from small intestine and deep sequenced to compare the gene expression profiles among WT, RIPK3-/- and Villin-cre RIPK3fl/fl.

overall_design: Duplicated 3 WT, 3 RIPK3-/- and 3 Villin-cre. RIPK3fl/fl acute GVHD small intestine samples were sequenced and compared.

first: Xiaoliang

last: Yu

first: Sudan

last: He

first: Siying

last: Liu


title: Chromatin and expression landscape of CLL cells with hyperactivated Notch1

type: Genome binding/occupancy profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Microarray profiling analysis of microRNAs expression  in NFATc3-overexpressed human monocyte-derived macrophages (HMDMs)

status: Public on Dec 04 2020

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

summary: We performed microRNA microarrays from total RNA extracted from HMDMs treated with NFATc3 adenovirus to identify potential targts of NFATc3.

overall_design: Determination of the differential miRNA levels in HMDMs


title: Single-cell RNA sequencing of human thymic samples

status: Public on Jan 11 2021

city: San Francisco

first: Audrey

last: Parent

address: 513 Parnassus Ave

department: Diabetes Center

institute: University of California, San Francisco

summary: The goal of this study is to profile stromal cells comprising the human thymus to better understand how this critical organ of the immune system is generated and how it supports the development of T lymphocytes and induction of self-tolerance.

overall_design:
Stromal cells isolated from two fetal (19 and 23 gestational weeks), two postnatal (6 day old and 10 month old), and one adult (25 year old) thymic samples were analyzed by single-cell RNA sequencing using the 10X Genomics platform.

Please note that the *H5AD files containing the preprocessed, normalized and annotated count data of three experiments have been added on Nov 19, 2021.

first: Jhoanne

middle: L

last: Bautista

first: Nathan

last: Cramer

first: Lauren

middle: E

last: Byrnes

first: Julie

middle: B

last: Sneddon

first: Chun

middle: J

last: Ye

first: Mark

last: Anderson

middle: V


title: Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis

status: Public on Dec 01 2020

city: New York

first: Joseph

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

summary: Restorative proctocolectomy with ileal pouch-anal anastomosis is a surgical procedure in patients with ulcerative colitis refractory to medical therapies. Pouchitis, the most common complication, is inflammation of the pouch of unknown etiology. To define how the intestinal immune system is distinctly organized in response to inflammation and to develop mechanistic hypotheses of pouchitis, we analyzed tissues from patients with and without pouchitis and from patients with ulcerative colitis using single-cell RNA sequencing. We examined pouch lamina propria CD45+ hematopoietic cells from intestinal tissues of ulcerative colitis patients with (n=15) and without an ileal pouch-anal anastomosis (n=11).  Further in silico meta-analysis was performed to generate transcriptional interaction networks and identify drug targets for patients with inflamed pouches. We identified a population of IL1B+ antimicrobial macrophages and FOXP3+/BATF+ T cells that are expanded in inflamed tissues, which we further validated in other single cell RNA-seq datasets from IBD patients. Cell type specific markers obtained from single-cell RNA-sequencing was used to infer representation from bulk RNA sequencing datasets, which further implicated antimicrobial macrophages expressing IL1B with S100A8/A9 calprotectin as being associated with inflammation, and Bacteroidiales and Clostridiales bacterial taxa. We found that non-responsiveness to anti-integrin biologic therapies in ulcerative colitis patients was associated with the signature of this antimicrobial macrophage population in a subset of patients.  This study identified conserved and distinct features of intestinal inflammation between parts of the small and large intestine undergoing similar inflammation conditions. Specifically, we relate inflammation of the pouch, a surgically constructed organ, to other inflammatory contexts throughout the gastrointestinal tract.

overall_design:
scRNA-seq of immune cells from inflamed UC and pouch patients. Please note that raw data are not provided as they are derived from human subjects.

**Raw data not provided due to patient privacy concerns**

first: Jordan

last: Axelrad

first: Ashley

last: Hine

first: Kelly

last: Ruggles

first: Ken

last: Cadwell

first: P'ng

last: Loke


title: Transcriptomic profiling of the liver from dnmt1 mutant zebrafish larvae compared to their phenotypically normal siblings at 120 hpf

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: In this dataset we performed RNA-seq on pools of livers dissected at 120 hpf from dnmt1(s904) mutants and phenotipically wild-type looking siblings.

overall_design: dnmt1-s904 (ABNYU background) hetorozygous zebrafish adults were incross to generate larvae. We collected 20-30 livers from each experimental group from 3 independent clutches of dnmt1-s904 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using triacane at 120 hours post fertilizaion (dpf). Livers were manually dissected under the stereomicroscope and put directly in Trizol for the following extraction. Total RNA was DNAseI treated, depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep.

first: Elena

last: Magnani

last: Edepli


title: RNA-Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers

summary: In this study, we performed RNA-seq on 5 dpf livers of uhrf1-hi272 mutants and phenotypically wild-type siblings collected at 120 hpf.

overall_design: "To perform RNA-seq on pools of uhrf1-hi272 mutant and sibling livers at 5 dpf, we collected between 15-30 livers from 5 independent clutches of uhrf1-hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol (https://www.thermofisher.com/ae/en/home/references/protocols/nucleic-acid-purification-and-analysis/mrna-protocols/trizol-plus-rna-purification-kit.html#prot2). Total RNA was DNAseI treated, depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single-end reads.

first: Anjana

last: Nair

first: Bhavani

last: Madakashira


title: RNAseq on uhrf1 zebrafish mutant larvae at 5 dpf compared to phenotypically normal siblings

summary: In this study, we performed RNA-seq on 5 dpf whole larvae of uhrf1-hi272  mutants and phenotypically wild-type siblings to determine changes in the transcriptomic profile.

overall_design: To perform RNA-seq on pools of whole larvae of uhrf1-hi272   mutants and siblings on 5 dpf, we collected between 10 and 20  larvae  from 2 independent  clutches of uhrf1-hi272 mutants their phenotypically WT siblings which were sorted based on phenotype following immobilization using triacane.  We  extracted total RNA  from the entire larvae to generate libraries, which were analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold.  cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single-end reads.

first: Yelena

last: Chernyavskaya


title: DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq]

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: DNA binding analysis of MYCs using Arabidopsis- and bHLH.specific Protein Binding Microarrays

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana
Solanum lycopersicum

overall_design: DAP-seq experiments

first: J


title: Neuronal-like differentiation of A549 cells in response to PRMT1 knockdown

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary:
Formerly we found that cancer-promoting factors, such as some typical epigenetic modification factors, are neural specific or enriched in embryonic neural cells, and play a key role in conferring the property of nerual stemness to cancer cells or in maintaining neural stemness in neural stem/progenitor cells. Our recent study demonstrated that PRMT1, a protein arginine methyltransferase, serves also to maintain neural stemness in either neural stem/progenitor cells or cancer cells.
We used microarray to analyze global gene expression change in A549 cells after PRMT1 knockdown.

overall_design: PRMT1 function was inhibited in A549 cells via shRNA knockdown. Cells showed significant morphological change after 8 days of PRMT1 knockdown compared with control cells that was infected with lentivirus carrying empty vector. Control and knockdown cells were then collected and subjected to microassay analysis. Two samples, one was control A549 cells and the other was the cells with PRMT1 knockdown, were used for microarray assay.

first: Lu

last: Chen


title: Chrom-Lasso：A lasso regression-based model to detect functional chromatin interactions using Hi-C data

status: Public on Nov 30 2020

city: Beijing

first: Jingzhe

last: Lu

state: Beijing

address: No.30 shuangqing road

department: School of medicine

institute: Tsinghua University

summary: We present Chrom-Lasso, an algorithm to identify chromatin interactions from Hi-C data, which performs better in identifying functional chromatin interactions that regulates gene expression when comparing with other methods. To futher assess its performance in investigating biological questions and its ability to deal with noisy data, we use an in vitro mouse CD8+ T cell activation model to generate Hi-C data and RNA-seq data at 4 status(Tn, Teff1, Teff2, Tex) during the process of activation, and we sort T cells at different status by gating criteria as follows: Tn(CD8+, CD44-, CD62L+, at day0), Teff1(CD8+, PD-1+, TIM-3-, at day2), Teff2(CD8+, PD-1+, TIM-3-, at day5), and Tex(CD8+, PD-1+, TIM-3+, at day5), for each status, we prepare 1 Hi-C library following the in situ Hi-C prorocol, and we also prepare 3 RNA-seq libraries from 3 times of parallel experiments. Since functional interactions influence the downstream gene expression level, so the relevance between interactions detected by Chrom-Lasso and gene expression would be powerful evidence proving the capability of Chrom-Lasso in detecting  functional interactions.

overall_design: In situ Hi-C was used to probe the interactions on 3D genome in 4 different status during the process of in vitro mouse CD8+ T cell activation, and RNA-seq was used to profile the change of gene expression during this process.

first: Xu

last: Wang

first: Keyong

last: Sun


title: Clonal expansion of CD8+ T cells reflects graft-versus-leukemia activity and precedes durable remission following DLI.

status: Public on Nov 16 2020

city: Hannover

first: Christian

last: Schultze-Florey

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: We show that an effective GvL is associated with a substantial drop of CD8+ TRB diversity and a concomitant expansion of dominant clones.

overall_design: TRB sequencing of sorted CD8+ T cells comparing leukemia patients with and without GvL effect after therapeutic DLI; SupplementalTables.docx containing sTable 1 "Patient samples" and sTable2 "Response to DLI"

first: Immo

last: Prinz

last: Koenecke

first: Leonie

last: Kuhlmann


title: Transcriptome analysis of initial cerebral responses following neurotropic virus infection reveals faulty innate immunity and delayed antigen presentation in mice susceptible to virus-induced demyelination

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: Viral infections of the central nervous system cause acute or delayed neuropathology and clinical consequences ranging from asymptomatic courses to chronic, debilitating diseases. The outcome of viral encephalitis is partially determined by genetically programmed immune response patterns of the host. Experimental infection of mice with Theiler’s murine encephalomyelitis virus (TMEV) causes diverse neurologic diseases, including TMEV-induced demyelinating disease (TMEV-IDD), depending on the used mouse strain. The aim of the present study was to compare initial transcriptomic changes occurring in the brain of TMEV-infected SJL (TMEV-IDD susceptible) and C57BL/6 (TMEV-IDD resistant) mice. Animals were infected intracerebrally with TMEV and sacrificed 4, 7 or 14 days post infection (dpi). Control animals of both strains were inoculated with vehicle only and sacrificed at 7 dpi. RNA was isolated from brain tissue and analyzed by whole transcriptome sequencing. Selected differences were confirmed on a protein level by immunohistochemistry. In mock-infected mice SJL and C57BL/6 mice, >200 differentially expressed genes (DEGs) were detected. Following TMEV-infection, the number of DEGs increased to >700. Infected C57BL/6 mice showed a higher expression of transcripts related to antigen presentation MHCI I, innate antiviral immune responses and cytotoxicity, compared to infected SJL animals. Many of those genes were also upregulated in SJL mice upon infection, but the response was weaker or delayed, which could be responsible for failure of viral clearance in this mouse strain. SJL mice showed prolonged elevation of MHC II and chemotactic genes, compared to C57BL/6 mice, which presumably facilitates the induction of chronic demyelinating disease. In addition, elevated expression of several genes associated with immunomodulatory or –suppressive functions was observed in SJL mice. The exploratory study confirms previous observations in the model and provides an extensive list of immunologic parameters potentially contributing to different outcomes of viral encephalitis in two mouse strains.

overall_design: Whole transcriptome sequencing of brain tissue derived from SJL and C57BL/6 mice following mock- or TMEV-infection.

first: Ciurkiewicz

last: Malgorzata

first: Floess

last: Stefan

first: Beckstette

last: Michael

first: Kummerfeld

last: Maren

first: Baumgärtner

last: Wolfgang

first: Huehn

last: Jochen

first: Beineke

last: Andreas


title: Profiling of ribose methylations in ribosomal RNA from diffuse large B-cell lymphoma patients for evaluation of ribosomes as drug targets

status: Public on Nov 13 2020

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Cancer cells are addicted to ribosome biogenesis and high levels of translation. Thus, differential inhibition of cancer cells can be achieved by targeting aspects of ribosome biogenesis or ribosome function. Using RiboMeth-seq for profiling of the ~112 2’-O-Me sites in human ribosomal RNA, we demonstrated pronounced hypomethylation at several sites in patient-derived DLBCL cell lines with a more severe perturbation in ABC-DLBCL compared to GBC-DLBCL. We extended our analysis to tumor samples from patients and demonstrated significant changes to the ribosomal modification pattern that appeared to consist of cell growth-related as well as tumor-specific changes. Sites of hypomethylation in patient samples are discussed as potential drug targets, using as an example a site in the small subunit (SSU-C1440) located in a ribosomal substructure that can be linked to DLBCL pathogenesis.

overall_design: Cell cultures were analyzed in biological triplicates, tissue and tumor samples in technical triplicates.

first: Fazila

last: Asmar

first: Christophe

last: Côme

first: Helga

last: Fibiger Munch-Petersen

first: Kirsten

last: Grønbæk

first: Henrik

last: Nielsen


title: DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs

first: Jose M.

last: Franco-Zorrilla

type: Genome binding/occupancy profiling by array

platform_organism:
Marchantia polymorpha
Arabidopsis thaliana
Solanum lycopersicum


title: Single Cell RNAseq on Renal adenocarcinoma

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

summary: We used droplet based Single cell RNA sequencing (10x genomics) on sorted cell from tumor and juxta tumor tissue to explore myeloid cell diversity and metabolism in tumor microenvironement

overall_design: We diggested tumor and juxtatumoral tissue and then performed flow sorting of myeloid cells. Cells were then encapsulated following manufacturer instructions

first: Rafael

last: Argüello

first: Alexis

last: Combes

first: Matthew

middle: F

last: Krummel


title: PD-1 independent of PD-L1 promotes glioblastoma growth through the NF𝜅B pathway

status: Public on Oct 30 2020

city: Calgary

first: Hena

middle: Rehman

last: Ramay

state: AB

address: 6 Erlton Terrace SW

department: International microbiome centre

country: Canada

institute: University of Calgary

summary: we found that a proportion of human and murine brain tumor-initiating cells (BTICs) expressed programmed cell death protein (PD-1) in situ and in culture. PD-1 signaling through NF𝜅B promotes BTIC proliferation.

overall_design: Human BTICs isolated from three GBM patients were transfected to overexpresss (OE) PD-1. Cells transfected with vector control were considered as OE control. Transfected cells (OE and OE controls) were subjected to bulk RNA sequencing.

first: Reza

last: Mirzaei

first: V

last: Yong


title: DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [PromData]

overall_design: Recombinant fusion proteins MBP-MYC2, MBP-MYC3, MBP-MYC4 and MBP-b17 were expressed in E. coli and incubated on bHLH-specific Protein Binding Microarrays (bHLH-PMBs)

first: Jose

middle: M


title: DNA methylation analysis by RRBS of WT and uhrf1-hi272 mutant zebrafish whole larvae at 5 dpf

last: Sadler Edepli

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a central repressive epigenetic mark. In this dataset we performed RRBS on whole zebrafish larvae from uhrf1-hi272 mutants and phenotypically wild-type siblings to determine which genomic regions have changes in DNA methylation due to uhrf1 loss.

overall_design: uhrf1-hi272 hetorozygous zebrafish adults were incross to generate larvae. We sorted uhrf1-hi272 mutants from their phenotypically WT siblings based on phenotype following immobilization using tricaine at 5 days post fertilizaion (dpf). We collected 10 whole larvae from each experimental group and extracted high molecular weight DNA using a DNA extraction buffer as previously described (Chernyavskaya et al., 2017). To compare efficacy of the RRBS protocol, we prepared two libraries using 50 or250 ng to perform RRBS library prep. Libraries were prepared according to Garrett-Bakelman et al., 2015, with the exception that the adaptors used for multiplexing were purchased separately (Next Multiplex Methylated Adaptors–New England Biolabs) and libraries were size selected by dual-step purification with Ampure XP Magnetic Beads (Beckman Coulter, Agencourt).

first: Filippo

last: Macchi

middle: C

last: Sadler


title: A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: After analysing auxin metabolism in auxin dependent tobacco BY-2 cell line grown in presence or absence of synthetic auxin 2,4-D we found that both conditions were similarly characterized by very low levels of endogenous indole-3-acetic acid (IAA) and its metabolites. However, metabolic profiling after exogenous application of IAA uncovered that the concentration of N-(2-oxindole-3-acetyl)-L-aspartic acid (oxIAA-Asp), the most abundantly formed auxin metabolite in the control culture, dramatically decreased in auxin-starved conditions. To describe the molecular mechanism behind this regulation, we analysed transcriptome and proteome changes caused by auxin starvation. While no changes in the expression of auxin biosynthetic machinery were observed, many genes related to auxin conjugation and degradation showed differential expression. Selected putative auxin glycosylating enzymes as well as members of the Gretchen Hagen 3 gene family involved in auxin amino acid conjugation showed both up- and down-regulation. Contrarily to that, all tobacco homologs of Arabidopsis thaliana DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), known to be responsible for the formation of oxIAA from IAA, showed significant downregulation at both transcript and protein levels.

overall_design: Seven biological replicates of Nicotiana tabacum L. cv. Bright Yellow (BY-2)  cell culture samples cultured at auxin supplemented conditions (ctrl) and three replicates of BY-2 cell culture samples cultured at auxin-starved (AF) conditions. Samples collected 48 hours after culture inoculation.

last: Müller

first: Jan

last: Petrášek


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [Chip-Seq + RNA-Seq]

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

summary: Multiple convergent pathways resulting in inhibition of the transcription factor EBF1 is a major cause of TERT upregulation.

overall_design: NanoChIP-seq, Capture-C, CapStarr-Seq and TF-ChIPSeq were integrated to study the regulation mechanisms of EBF1 and TERT expression in gastric cancer.

first: Manjie

last: Xing

first: Ooi

last: Fong

first: Patrick

last: Tan


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [RNA-seq]


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [ChIP-Seq - EBF1, EZH2]


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [histone]


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [CapStarr-seq]


title: Identification of genes showing an age related expression in iNKT1, 2, and 17 cells of BALB/c thymus

status: Public on Oct 26 2020

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

summary:
In this study we applied RNA high-throughput seqencing to compare the global gene expression of young adult and aged iNKT subset in thymus of BALB/c mice.
We found that only a small number of genes exerted a profound and statistically significant up- or downregulation upon ageing whereas a plethora of minor changes in the gene expression pattern were evident. However, significant age-related differences in expression of a variety of genes such as Histone genes, Gzma, CD25 and others might
correlate with functional adaptations to the drastically altering thmyus micro-environment during aging.

overall_design: Surface markers CD4 and CD122 were used to sort by flow cytometry CD3+tet+DAPI-B220- thymocytes of young adult and aged BALB/c mice to obtain iNKT1, iNKT2 and iNKT17 cells. Total RNA was prepared and quality controlled aliquots used for sequencing.

first: Georgia

last: Papadogianni

first: Hristo

last: Georgiev


title: DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [GenomeData]

first: Jose M.

last: Franco-Zorrilla

overall_design: Recombinant fusion proteins MBP-MYC2, MBP-MYC2, MBP-MYC2 and  MBP-b17 were expressed en E. coli and incubated on bHLH-specific Protein Binding Microarrays (bHLH-PMBs)


title: Whole-body-vibration training positively affects muscle transcriptome in tumour bearing cachectic mice

status: Public on Nov 01 2020

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Background The prevailing view is that a combination of nutritional, pharmacological and exercise therapy is most optimal to reduce the development and progression of cancer cachexia. However, in many cancer patients, physical activity is hampered by frailty and fatigue. The present study aimed to investigate whole-body vibration training (WBV) as potential alternative to attenuate loss of weight, muscle mass and function in tumour bearing mice. Methods Twenty-four male CD2F1-mice (21.5±0.2g) were stratified into four groups (control=[C], control+WBV=[C+V], tumour-bearing=[T] and tumour-bearing+WBV=[T+V]), and injected  (day 1) with C26 cells or vehicle. From day 1, whole-body-vibration (WBV groups) was performed for 19 days (15min, 45Hz, 1.0g acceleration). General outcome measures included body mass and composition, and daily activity. In addition, blood analysis and assessments of muscle histology and function and whole genome gene expression in m. soleus (SOL) and m. extensor digitorum longus (EDL) were performed. Two-way ANOVA with factors tumour, training and interaction was used for statistical analysis. Results Body weight, lean and fat mass and EDL mass were all lower in tumour bearing mice compared to controls. No effects of vibration training were found on systemic cachexia related outcomes. However, WBV increased EDL mass in the control treatment,. SOL mass did not differ, whereas SOL function was affected by both tumour and WBV. Interestingly, WBV reduced the tumour-related effects on muscle gene expression in EDL, SOL and heart. Conclusions These data suggest that WBV had only minor effects on cachexia related outcomes in the present experimental set-up, while muscle transcriptome was positively affected. This merits follow-up studies applying for example longer treatment periods or incorporating WBV in a multiple-target intervention.

overall_design: Microarray analysis was performed on skeletal muscle biopsies (m. soleus, m. extensor digitorum longus and heart) from mice with or without cachexia and/or whole body vibration training.

first: Rogier

last: Plas

first: Miriam

last: van Dijk

first: Jvalini

middle: T

last: Dwarkasing

first: Frans

last: van Gemerden

first: Hans

last: Swarts

first: Evert

last: van Schothorst

first: Renger

last: Witkamp

first: Klaske

last: van Norren


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [Capture-C]

first: Wen Fong

last: Ooi


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer [ChIP-Seq - H3K27me3]

first: Manjie

last: Xing


title: Transcription factor C/EBPβ orchestrates DC maturation and functionality under homeostatic and malignant conditions [CEBPbetaKO]

status: Public on Oct 20 2020

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Dendritic cell (DC) maturation is a prerequisite for the induction of adaptive immune responses against pathogens and cancer. Transcription factor (TF) networks control differential aspects of early DC progenitor versus late stage DC cell fate decisions. Here, we identified the TF C/EBPβ as a key regulator for DC maturation and immunogenic functionality under homeostatic and lymphoma-transformed conditions. Gene expression profiles of splenic C/EBPβ-/- DCs showed a strong downregulation of E2F cell cycle target genes, whereas signatures of maturation were enriched. In accordance with E2F1 being a negative regulator of DC maturation, C/EBPβ-/- bone marrow-derived DCs matured much faster enabling them to strongly activate T cells. Conversely, the E2F transcriptional pathways were upregulated in lymphoma-exposed DCs and DC maturation was impaired. Pharmacological blockade of C/EBPβ/mTOR signaling in human DCs abrogated their pro-tumorigenic function in B-cell lymphoma co-cultures. Thus, C/EBPβ plays a unique role in DC maturation and functionality and emerges as a key factor of the microenvironment promoting lymphomagenesis.

overall_design: To test the role of C/EBPβ in the regulation of DC maturation and cell fate decision under homeostatic conditions, we employed genome-wide expression profiling of C/EBPβ-proficient and C/EBPβ-deficient murine DC cells. Splenic CD11c+MHCII+ DCs were sorted from CD11c-Cre-eGFP (C/EBPβ+/+) and from CD11c-Cre-eGFPxC/EBPβflox/flox (C/EBPβ-/-) mice. Furthermore, a downregulation of C/EBPβ was recently observed, when we exposed DCs to lymphoma cells in the murine aggressive Myc-driven B cell lymphoma model. Based on these data, we analyzed whole genome transcriptional changes in DCs upon exposure to Eµ-Myc lymphoma cells.

first: Uta

last: Höpken


title: Transcription factor C/EBPβ orchestrates DC maturation and functionality under homeostatic and malignant conditions

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcription factor C/EBPβ orchestrates DC maturation and functionality under homeostatic and malignant conditions [Emu-Myc]


title: Genomic and Epigenomic EBF1 Alterations Modulate TERT Expression in Gastric Cancer


title: Genome-wide identifying of G-quadruplex structures directly by whole-genome resequencing

status: Public on Oct 10 2020

city: NanJing

first: Tu

last: Jing

state: JiangSu

address: Si Pailou

department: Biological Science and Medical Engineering

institute: South East University

summary: G-quadruplex (G4) structure is an alternative conformation of the double helical structure of B-form DNA arisen in guanine-rich sequences . The formation of G4 structures can influence chromatin architecture and many fundamental biology processes, such as DNA replication and gene regulation . We present G4-miner, a genome-wide approach to directly identify G4 structures from ordinary sequencing data. G4-miner inspects sequencing quality in whole genome, seizes unexpected fluctuations in local, and ascribes some of the quality fluctuations to the unstable formation of G4. We identified 736,689 G4 structures within human genome, in which 44.9% of all predicted canonical G4-froming sequences were contained.

overall_design: 2 library samples of primary human B lymphocytes

first: Jing

last: Tu

first: Mengqin

last: Duan

first: Wenli

last: Liu

last: Lu


title: Transcriptomic profile of a skeletal muscle model of Pompe disease and recombinant protein therapy

status: Public on Oct 06 2020

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomic profile of skeletal muscle in wild-type, GAA knock-out, and AAV treated GAA knock-out mice to understand Pompe disease mechanisms and assess therapeutic efficacy

summary: Pompe disease (glycogen storage disease type II, or acid maltase deficiency) is an autosomal-recessive disorder of metabolism caused by mutations in the lysosomal hydrolase, acid alpha-glucosidase gene (GAA), resulting in progressive muscle atrophy. Gene therapy is a promising approach to treat genetic diseases, and liver-restricted expression of secretable GAA can produce immune tolerance and improve muscle GAA activity. To further understand the molecular mechanisms underlying Pompe disease and impact of gene therapy, we applied RNA sequencing.

overall_design: High throughput sequencing of RNA obtained from the quadriceps of wild-type, GAA (acid alpha glucosidase) knock-out mice, and AAV-treated GAA-knock out mice.

first: Nenad

last: Bursac

first: Jason

last: Wang

first: Dwight

middle: D

last: Koeberl

first: Priya

last: Kishnani


title: Transcriptomic profile of three-dimensional tissue-engineered human skeletal muscle model of Pompe disease and recombinant protein therapy

summary: Pompe disease (glycogen storage disease type II, or acid maltase deficiency) is an autosomal-recessive disorder of metabolism caused by mutations in the lysosomal hydrolase, acid alpha-glucosidase gene (GAA), resulting in progressive muscle atrophy. The current standard of care treatment, enzyme replacement therapy, consists of delivering recombinant human GAA (rhGAA) to reduce muscle glycogen and improve patient quality of life.  With the aim of developing in vitro systems to study human disease and test therapies, we applied RNA sequencing to 3D tissue-engineered human skeletal muscle to compare healthy, (infantile onset) Pompe disease, and rhGAA-treated Pompe engineered tissues.

overall_design: High throughput sequencing of RNA obtained from healthy, Pompe disease, rhGAA treated Pompe disease engineered skeletal muscle


title: Transcriptome profiling of mice lungs exposed to low-dose ricin .

status: Public on Oct 14 2020

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary:
The goal of this study is to explore the alterations in gene expression in lungs of mice 48 hours after exposure to low-dose ricin compared to lungs of naive mice, in order to provide a framework for comparative investigation of genes and mechanisms that may contribute to the developing lung disease.
Methods: Total RNA was extracted from lungs of naive or ricin intoxicated mice (intranasally exposure to 1.7 µg/kg ricin), using the RNeasy mini kit (Qiagen). RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 21M reads per sample that were mapped to the mouse genome. The expression of the infected sample was compared to mock sample, and RNA ratios were clustered using partitioning clustering.  We next carried out GO term enrichment analysis.
Results: Principal component analysis revealed distinct transcriptional signatures between naïve and ricin mice. We found 8545 differentially expressed genes in the ricin group, including 4394 upregulated and 4151 downregulated genes.

overall_design: Examining the alterations in gene expression in lung of mice after intranasal exposure to low-dose ricin

first: Reut

last: Falach

first: Ofir

last: Israeli

last: Gihon

first: Galia

last: Zaide

first: Dana

last: Stein

first: Yentle

last: Ivgi

first: Moshe

last: Aftalion

first: David

last: Gur

first: Tamar

last: Sabo

first: Chanoch

last: Kronman


title: Comparison of whole blood transcriptional changes induced by menignoccocal capsular group B vaccines in mice

status: Public on Oct 16 2020

city: Oxford

first: Dylan

last: Sheerin

address: Churchill Hospital, Old Road

country: United Kingdom

institute: University of Oxford

summary: Whole blood RNA-seq was leveraged to explore gene expression changes induced in mice 24 hours after immunisation with a second dose of a licensed vaccine against capsular group B meningococcus, one of the vaccines components, or one of several comparator groups.

overall_design: mRNA was profiled from RNA extracted from mouse whole blood, 3-6 samples per group, using an Illumina HiSeq4000


title: Molecular signatures of inflammatory profile and B-cell function in SFTS patients

status: Public on Oct 01 2020

city: Los Angeles

first: Angela

last: Park

state: CA

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Severe fever with thrombocytopenia syndrome banyangvirus (SFTSV) induces immunopathogenic disease with high fatality rate. Despite serious health concern, the mechanisms underlying clinical manifestations are largely unknown. Here, we applied targeted proteomics and single-cell transcriptomics analyses to examine the differential immune landscape of SFTS patient blood. Serum immunoprofiling distinguished Low-risk and High-risk clusters of SFTS patients with differential inflammatory cytokine levels, which matched with disease severity. Single-cell transcriptomics analysis of SFTS patient blood at different infection state showed pronounced expansion of B cells with the alteration of B-cell subset populations, specifically in fatal patients. Furthermore, plasma cells were the primary reservoir of SFTSV replication with the downregulation of IFN pathway. This study identifies not only the molecular signatures of serum inflammatory profile and B cell lineage population, but also plasma cells as the viral reservoir in SFTSV-induced fatal patients, suggesting the alteration of B cell function linked to SFTS lethal infection.

overall_design: PBMC from Control, Infection, Recovery and Fatal SFTS patients were collected in hospitals throughout South Korea. PBMC from each individual were processed separately through the ChromiumTM Single Cell Platform with the 10X Genomics ChromiumTM Single Cell 3’ Library and Gel Bead Kit v2 and the Chromium Single Cell A Chip Kit  using the standard manufacturer’s protocol.

first: Kyle

last: Jung

first: Jae

middle: U

first: Young

middle: K

last: Choi


title: Profound effect of a small cysteine-free protein (pspA) on genomic expression of Beauveria bassiana

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

summary:
Purpose: This transcriptomic analysis aims at unveiling all possible genes orchestrated by pspA, which is evidently required for insect pathogenicity and virulence-related cellular events of Beauveria bassiana.
Methods: Total RNAs were extracted from three 3-day-old hyphal cultures (replicates) of pspA disruption and wild-type strains grown under normal culture conditionsand and subjected to deep sequencing on Illumina NovaseqTM 6000 platform. The sequence reads that passed quality filters were mapped to the genome of Beauveria bassiana. All genes differentially expressed in the disruptant versus the wild-type strain were enriched to GO function classes and KEGG pathways.
Results: The resultant transcriptome comprises 10430 genes annotated or not annotated. Among those, 1818 genes (genomic 17.54%) were dysregulated in the absence of pspA, including 806 down-regulated and 1012 up-regulated.
Conclusions: pspA lacking any predictable function domain has profound impact on the genomic expression of Beauveria bassiana.

overall_design: RNA profiles from 3-day-old hyphal cultures of pspA disruption and wild-type strains.

first: Ya-ni


title: Integration of Metabolomics and Transcriptomics Reveals Changes in MRSA Exposed to Terpinen-4-ol

status: Public on Sep 09 2020

city: lanzhou

first: feng

last: cheng

state: GanSu

address: 335 Qilihe Rd,

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences

summary: Staphylococcus aureus (S. aureus) is a gram-positive bacterium that causes a wide range of diseases. Terpinen-4-ol is a monoterpene component contained in most plant essential oils with good antibacterial activity. In this study, terpinen-4-ol effectively inhibited 13 strains of S. aureus, and effectively inhibited the biofilm of MRSA. Metabolomics and transcriptomics were used to elucidate changes in MRSA cells exposed to terpinen-4-ol. Terpinen-4-ol significantly changed (greater than a 2- or less than a 2-fold change) the expression of 304 genes and the level of 847 metabolites (greater than a 1.5- or less than a 0.67-fold change) in MRSA. The levels of genes and metabolites related to the valine, leucine and isoleucine biosynthesis metabolism pathway, the purine and pyrimidine metabolism pathway, energy metabolism and β-lactam resistance were dramatically changed in biofilms exposed to terpinen-4-ol. To the best of our knowledge, this research is the first to report the metabolite and expression profiles of MRSA exposed to terpinen-4-ol.

overall_design: Use 0.08% terpinen-4-ol to treat MRSA ATCC43300

first: Cheng

last: Feng

first: Liu

last: Yu

first: Mo

last: Yanan

first: Liang

last: Jianping


title: L-bodies are novel RNA-protein condensates driving RNA transport in Xenopus oocytes

status: Public on Sep 20 2020

city: Providence

first: Kimberly

last: Mowry

state: RI

address: 185 Meeting Street

department: MCB

institute: Brown University

summary: RNP granules are membrane-less compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes.  However, the mechanisms by which RNAs and proteins interact to promote RNP granule assembly and function in vivo remain unclear.  In Xenopus laevis oocytes, maternal mRNAs are transported as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning.  Here, we demonstrate that vegetal transport RNPs represent a new class of cytoplasmic RNP granule, termed Localization-bodies (L-bodies).  We show that L-bodies are multiphase RNP granules, containing a dynamic liquid-like protein-containing phase surrounding a non-dynamic RNA-containing substructure.  Our results support a role for RNA as a critical scaffold component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.

overall_design: 4 replicates of 3 conditions were analyzed, the conditions being RNA collected after immunoprecipitating Xenopus oocyte lysates with different antibodies. The experimental conditions were precipitated with Staufen and hnRNPab antibodies and the control condition precipitated with IgG.

first: Christopher

middle: R

last: Neil

first: Samantha

middle: P

last: Jeschonek

first: Sarah

last: Cabral

first: Liam

last: O'Connell

first: Jessica

last: Otis

first: Erin

middle: A

last: Powrie

first: Timothy

last: Wood


title: Far-red enriched light delays tomato transcriptome modulations in response to Botrytis cinerea infection

status: Public on Sep 30 2020

city: Utrecht

last: Courbier

address: Padualaan 8

department: Biology

institute: Utrecht University

summary: We performed a transcriptome analysis of a 30 -hour infection time course aiming to unravel hormonal and metabolic pathways affected by FR which would in turn modulate disease resistance. Our data show that supplemental FR, received before pathogen inoculation, triggers the FR-induced susceptibility, which is associated with a delay in pathogen recognition and defense activation via JA and possibly ethylene signaling. The transcriptome analysis highlighted a set of six PROTEINASE INHIBITOR genes (PI) that are induced only in WL-treated samples. As PI genes are described to be JA-responsive genes, the FR-induced susceptibility in tomato is possibly due to a dampening of JA-mediated gene induction and expression affecting defense responses resulting in more susceptible plants.

overall_design: We examined the transcriptional response of tomato leaves subjected to either white or far-red enriched light prior to inoculation with the necrotrophic fungus Botrytis cinerea or a mock solution. We then followed the transcriptome changes through time (every 6 hours from 0 to 30 hours post inoculation).

first: Basten

last: Snoek

first: Kaisa

last: Kajala

first: Saskia

last: Van Wees

first: Ronald

last: Pierik


title: Transcriptomic signature of fasting in adipose tissue

status: Public on Sep 01 2020

first: Guido

last: Hooiveld


title: Transcriptomic signature of fasting in murine adipose tissue

summary: Little is known about the impact of fasting on gene regulation in human adipose tissue. Accordingly, the objective of this study was to investigate the effects of fasting on adipose tissue gene expression in humans. To that end, subcutaneous adipose tissue biopsies were collected from volunteers 2h and 26h after consumption of a standardized meal. For comparison, epididymal adipose tissue was collected from C57Bl/6J mice after a 16h fast and in the ab-libitum fed state. Transcriptome analysis was carried out using Affymetrix microarrays. We found that, 1) fasting downregulated numerous metabolic pathways in human adipose tissue, including triglyceride and fatty acid synthesis, glycolysis and glycogen synthesis, TCA cycle, oxidative phosphorylation, mitochondrial translation, and insulin signaling; 2) fasting downregulated genes involved in proteasomal degradation in human adipose tissue; 3) fasting had much less pronounced effects on the adipose tissue transcriptome in humans than mi  ce; 4) although major overlap in fasting-induced gene regulation was observed between human and mouse adipose tissue, many genes were differentially regulated in the two species, including genes involved in insulin signaling (PRKAG2, PFKFB3), PPAR signaling (PPARG, ACSL1, HMGCS2, SLC22A5, ACOT1), glycogen metabolism (PCK1, PYGB), and lipid droplets (PLIN1, PNPLA2, CIDEA, CIDEC). In conclusion, although numerous genes and pathways are regulated similarly by fasting in human and mouse adipose tissue, many genes show very distinct responses to fasting in humans and mice. Our data provide a useful resource to study adipose tissue function during fasting.

overall_design:
Microarray analysis was performed on gonadal adipose tissue in the fed or after a 16 hours fast:
Three to four month old C57BL/6 mice were fasted for 16 hours or fed ad libitum. Gonadal white adipose tissue was collected to find changes in gene expression upon fasting in the white adipose tissue.

first: Merel

last: Defour

first: Charlotte

last: Michielsen

first: Lydia

last: Afman

first: Sander

last: Kersten


title: B cell-derived IL35 drives STAT3-Dependent CD8+ T-cell Exclusion in Pancreatic Cancer

status: Public on Aug 28 2020

city: Chapel Hill, NC

first: Yuliya

last: Pylayeva-Gupta

address: 450 West Drive, CB 7295

department: Lineberger Comprehensive Center

institute: UNC

summary: This study is designed to understand the role of immunosuppressive regulatory B cells (Breg) in pancreatic cancer.  Breg and conventional B cells (Bcon) from patients are compared by RNA sequencing analysis.

overall_design: Examination of differentially expressed genes in two blood-derived B cell subsets from a Pancreatic Ductal Adenocarcinoma (PAAD) patient.

first: Ben

middle: G

last: Vincent

first: Joel

middle: S

last: Parker


title: FLCN Gene Ablation Reduces Fibrosis and Inflammation in a Diet-Induced NASH Model

status: Public on Aug 27 2020

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: Non-alcoholic steatohepatitis (NASH) represents a major economic burden and is characterized by triglyceride accumulation, inflammation, and fibrosis. No pharmacological agents are currently approved to treat this condition. Emerging data suggests an important role of autophagy in this condition, which serves to degrade intracellular lipid stores, reduce hepatocellular damage, and dampen inflammation. Autophagy is primarily regulated by the transcription factors TFEB and TFE3, which are negatively regulated by mTORC1. Given that FLCN is a mTORC1 activator, we generated a liver-specific Flcn knockout mouse model to study its role in NASH progression. We demonstrate that loss of FLCN results in reduced triglyceride accumulation, fibrosis, and inflammation in mice exposed to a NASH-inducing diet. Furthermore, this study identifies a potential mechanism for NASH protection through autophagy activation resulting from the loss of FLCN. These results show an unexpected role for FLCN in NASH progression and highlight new possibilities for treatment strategies through its role in hepatocyte homeostasis.

overall_design: RNA sequencing data from livers of 3-months old Alb-cre WT (Cre) and Alb-cre FLCN KO (FLCN KO) mice, fed either on chow or methionine/choline deficient diet (MCD) for six weeks

first: Mathieu

last: Paquette

first: Leeanna

last: El-Houjeiri

first: Marco

last: Biondini

first: Ming

last: Yan

first: Josué

last: Ramírez-Reyes

first: Hyeonju

last: Jeong

first: Jennifer

middle: L

last: Estall

first: Peter

last: Siegel

first: Arnim

last: Pause


title: RNA profiling of laser microdissected human trophoblast subtypes at mid-gestation

status: Public on Aug 25 2020

city: SAN FRANCISCO

first: Susan

last: Fisher

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary: Human placental architecture is complex. Its surface epithelium, specialized for transport, forms by fusion of cytotrophoblast progenitors into multinucleated syncytiotrophoblasts. Near the uterine surface, these progenitors assume a different fate, becoming cancer-like cells that invade its lining and blood vessels. The latter process physically connects the placenta to the mother and shunts uterine blood to the syncytiotrophoblasts. Isolation of trophoblast subtypes is technically challenging. Upon removal, syncytiotrophoblasts disintegrate and invasive cytotrophoblasts are admixed with uterine cells. We used laser capture to circumvent these obstacles. This enabled isolation of syncytiotrophoblasts and two subpopulations of invasive cytotrophoblasts—cell column and endovascular. Transcriptional profiling revealed numerous genes whose placental or trophoblast expression was not known, including neurotensin and C4ORF36. Using mass spectrometry, discovery of differentially expressed mRNAs was extended to the protein level. We also found that invasive cytotrophoblasts expressed cannabinoid receptor 1. Unexpectedly, screening agonists and antagonists showed signals from this receptor promote invasion. Together these results revealed novel gene expression patterns that translate to the protein level. Our data also suggested that endogenous and exogenous cannabinoids can affect human placental development.

overall_design: This was a cross-sectional analysis of placentas collected at mid-gestation(n=4). Laser microdissection enabled the isolation of samples that were enriched for syncytiotrophoblasts, villus cytotrophoblasts or endovascular cytotrophoblasts. A microarray approach was used for global transcriptional profiling.

first: M

last: Gormley

first: O

last: Oliverio

first: Y

last: Zhou

last: Kapidzic

first: K

last: Ona

first: S

last: Hall


title: ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives HCC metastasis [RNA-seq]

status: Public on Aug 24 2020

city: Shanghai

first: Ze-Guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: ARID1A, encoding a subunit of SWI/SNF chromatin remodeling complex, is widely recognized as a tumor suppressor gene in multiple tumor types including hepatocellular carcinoma (HCC). Previous studies have demonstrated that ARID1A deficiency can cause HCC metastasis, possibly due to the altered chromatin organization, however the underlying mechanisms of which remain poorly understood. Whether and how SWI/SNF complex could function as an architectural cooperator to synergistically stabilize chromatin organization should be explored, particular in tumorigenesis. Here we reveal that SWI/SNF complex acts as a potential architectural cooperator via BRG1-RAD21 axis for chromatin organization maintenance; ARID1A deficiency weakens the interaction and thus loosens chromatin compactness, which drives HCC metastasis dependent on the conformational dysregulation on some key genes.

overall_design: Transcriptomic profiles of AB17 mouse hepatocytes with Ad-GFP (Wild type, WT) and Ad-Cre (Knockout, KO, Arid1a-/-) infection.

first: Zeguang

first: Yi

last: Shi

first: Xueying

last: Shang


title: ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives HCC metastasis


title: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [EG_SERIES_3]

status: Public on Aug 13 2020

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

summary: A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting protective versus detrimental immunity to pathogens that cause chronic infections such as Mycobacterium tuberculosis (Mtb). We have shown that systemic administration of BCG or b-glucan reprograms HSCs in the BM via a type II interferon (IFN-II) or IL1 response, respectively, that confers protective trained immunity against Mtb. Yet, whether BCG/β-Glucan is unique in its ability to induce this protection remains unknown. Herein, we demonstrate that unlike BCG or b-glucan, Mtb reprograms HSCs via IFN-I response that suppresses myelopoiesis and impairs protective trained immunity to Mtb. Mechanistically, IFN-I response dysregulates iron metabolism, depolarizes mitochondrial membrane potential, and induces cell death in myeloid progenitors. Finally, activation of IFN-I/iron axis in myeloid progenitors generates a detrimental trained immunity to Mtb infection. These results identify an unanticipated immune evasion strategy of Mtb in the bone marrow that controls the magnitude and anti-microbial capacity of innate immunity to infection

overall_design: Single cell RNA expression profiles of LKS+, and cKit+ progenitor cells of C57BL/6J mice subject to a secondary engraftment experiment.

first: Nargis

last: Khan

first: Jeffrey

last: Downey

first: Joaquín

last: Sanz

first: Eva

last: Kaufmann

first: Birte

last: Blankenhaus

first: Alain

last: Pacis

first: Erwan

last: Pernet

first: Eisha

last: Ahmed

first: Silvia

last: Cardoso

first: Anastasia

last: Nijnik

first: Bruce

last: Mazer

first: Christopher

last: Sassetti

first: Marcel

last: Behr

first: Miguel

last: Soares

first: Maziar

last: Divangahi


title: Gene expression analysis of 120 hpf zebrafish livers following 24 hour iAs exposure

status: Public on Aug 22 2020

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

institute: New York University Abu Dhabi

summary: This study was carried out to compare the changes in the gene expression in the liver of 5 day post fertilization zebrafish larvae in response to 24 hour exposure to 1.0 and 1.5mM iAs and to compare this to changes in gene expression as a result of overexpress as3mt in hepatocytes.  CL1 CAAX 1.5 = WT larvae exposed to 1.5 mM iAs; CL2 CAAX 1 = WT larvae exposed to 1.5 mM iAs

overall_design: The samples in this series include only livers from 120 hpf zebrafish larvae that were exposed to 1 and 1.5 mM of inoragnic arsenic (iAs) from 96 - 120 hpf. This study was carried out by comparing RNA extracted from 120 hpf zebrafish livers from six groups: untreated or 24-hour exposure to 1 mM or 1.5 mM iAs in CAAX-EGFP positive larvae and CAAX-EGFP positive and as3mt overexpressing larvae. To generate these samples ,(tg:(fab10a:as3mt, cry:dsRed) were outcrossed to tg(fabp10a:CAAX-EGFP) and the larvae that only had the CAAX-EGFP expression in the liver and cry:dsRed in the eye were collected.  RNA from 12 livers per group collected from 5 clutches (biological replicates) per group were extracted using Trizol/Chlorofom, PolyA selected and sequenced on Illumina NextSeq550. The control samples are contained in series GSE156412.


title: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis

first: Luis

last: Barreiro

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives HCC metastasis [ChIP-seq]

first: Ze-Guang

last: Han

overall_design: ChIP-sequencing on AB17 mouse hepatocytes with Ad-GFP (Wild type, WT) and Ad-Cre (Knockout, KO, Arid1a-/-) infection.

first: Zeguang

first: Yi

last: Shi

first: Xueying

last: Shang


title: DREAM represses distinct targets by cooperating with different THAP domain proteins [RNA-seq]

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

summary: The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z. Furthermore, the function of DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses a subset of germline targets by facilitating H3K9me2 promoter marking. In humans, THAP proteins have been implicated in cell cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function, facilitating repression of distinct sets of targets.

overall_design: 31 single-end, unstranded RNA-seq libraries were generated from polyA-selected RNA from starved L1 C. elegans strains (wt and mutants).

first: Csenge

last: Gal

first: Francesco

middle: N

first: Alex

last: Appert

first: Chiara

last: Cerrato

first: Ni

last: Huang

first: Yan

last: Dong

first: Jane

last: Murphy

first: Julie

last: Ahringer


title: Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

status: Public on Aug 14 2020

city: Ithaca

first: Charles

middle: Grahe

last: Danko

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

summary: The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 was 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observed multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in several non-immune tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.

sample_organism:
Macaca mulatta
Papio anubis

platform_organism:
Macaca mulatta
Papio anubis

overall_design: Hi-C and MicroC experiments from blood-derived CD4+ T-cells of rhesus macaque (Macaca mulatta). RNA-seq experiments from blood-derived CD4+ T-cells and CD14+ monocytes of rhesus macaque (Macaca mulatta) and baboon (Papio anubis).

first: Lauren

last: Choate

first: Gilad

last: Barshad


title: Single cell RNAseq analysis of mouse AAA sample

status: Public on Aug 04 2020

city: New York

first: Michele

last: Silvestro

address: 550 1st Avenue

department: Surgery

institute: New York University Langone Medical Center

summary: We report the application of single-cell-based RNA sequencing technology for high-throughput profiling of mice abdominal aortic aneurysm cell type dependent transcriptome. This study provides insight in the expression profile of aortic tissue macrophages in pathological conditions related to cardiovascular diseases.

overall_design: Examination of cell specific transcriptomes in highly Aneurysmal abdominal aorta single cell suspensions from an Apolipoprotein deficient mouse perfused for 28 days with angiotensin II

first: Bhama

last: Ramkhelawon


title: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [Bulk_SERIES_1]

first: Luis

last: Barreiro

overall_design: Bulk RNA expression profiles of Multipotent progenitors (MPPs) and hematopoietic stem cells (HSCs) of mice injected -iv with either BCG, M.tuberculosis or PBS.

first: Nargis

last: Khan

first: Jeffrey

last: Downey

first: Joaquín

last: Sanz

first: Eva

last: Kaufmann

first: Birte

last: Blankenhaus

first: Alain

last: Pacis

first: Erwan

last: Pernet

first: Eisha

last: Ahmed

first: Silvia

last: Cardoso

first: Anastasia

last: Nijnik

first: Bruce

last: Mazer

first: Christopher

last: Sassetti

first: Marcel

last: Behr

first: Miguel

last: Soares

first: Maziar

last: Divangahi


title: DREAM represses distinct targets by cooperating with different THAP domain proteins

first: Francesco Nicola

last: Carelli


title: Genome-wide profiling for H2A.Z and genome accessibility using ATACseq in  Uhrf1hepKO mouse livers compared to WT livers

status: Public on Jul 17 2020

first: Kirsten

last: Sadler Edepli

summary: This study was carried out to investigate potential changes in the genome-wide distribution of  H2AZ and genome accessibility using ATACseq in livers where Uhrf1 is deleted in hepatocytes (Uhrf1-fl/fl;Alb:Cre)  compared to controls (Uhrf1-fl/fl).

overall_design:
ChIP was carried out to pull down H2AZ bound chromatin from nuclei isolated from s single Uhrf1-Fl/fl liver and a single  (Uhrf1-fl/fl;Alb:Cre) male liver between 8-12 weeks of age. This chromatin fraction was then digested using micrococcal nuclease to release mononucleosomes. DNA fragments purified from nucleosomes were then used to generate libraries and sequenced. The same livers were used for chromatin
 accessibility using the ATAC-seq Protocol as described in Buenrostro et al (2015).

first: Shuang

last: Wang

first: Chi

last: Zhang

last: Sadler (Edepli)

first: Bhavani

last: Madakashira

first: Elena

last: Magnani


title: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [AERO_SERIES_2]

first: Luis

last: Barreiro

overall_design: Single cell RNA expression profiles of LKS+, and cKit+ progenitor cells of Control mice, and mice subject to an aerosol challenge with M.tuberculosis.

first: Nargis

last: Khan

first: Jeffrey

last: Downey

first: Joaquín

last: Sanz

first: Eva

last: Kaufmann

first: Birte

last: Blankenhaus

last: Pacis


title: Pioglitazone ameliorates gentamicin ototoxicity by affecting the TLR and STAT pathways in the early postnatal organ of Corti

status: Public on Sep 24 2020

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: We evaluated the effects of pioglitazone in mouse organ of Corti  (OC) explants to characterize its influence on signaling pathways involved in auditory hair cell damage. Organ of Corti explants were cultured with pioglitazone, gentamicin, or a combination of both agents. Pioglitazone treatment resulted in a significant repression of interferon (IFN)-alpha and -gamma pathways and downstream cytokines, as assessed by RNA sequencing and quantitative PCR gene expression assays. More detailed investigation at the single gene and protein level showed that pioglitazone mediated its anti-inflammatory effects through alterations of the Toll-like receptor (TLR) and STAT pathways. Together, these results indicate that pioglitazone significantly represses IFN and TLR in the cochlea, dampening the activity of gentamicin-induced pathways. These data support our previous results demonstrating significant protection of auditory hair cells in organ of Corti explants exposed to pioglitazone and other PPAR-targeted agents.

overall_design: Examination of pioglitazone, gentamicin or combined treatment effects on signalling pathway changes in the early postnatal wild type Organ of Corti explants.

first: Marijana

last: Sekulic

first: Robert

last: Ivanek

first: Daniel

last: Bodmer


title: Analysis of serum exosomal miRNAs associated with lymph node metastasis in esophageal squamous cell carcinoma

status: Public on Jul 30 2020

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: Preoperative prediction of lymph node (LN) metastasis is accepted as an important independent risk factor for treatment decision-making for esophageal squamous cell carcinoma (ESCC) patients. This study aimed to develop a non-invasive biomarker to identify LN metastasis preoperatively in ESCC patients with serum exosomal RNA-seq.

overall_design: RNA-seq of serum exosomal RNA collected from ESCC patients with or without lymph node metastasis.

first: Chuanxin

first: Tong

last: Liu

first: Lutao

last: Du

first: Yunshan

first: Juan

last: Li


title: DREAM represses distinct targets by cooperating with different THAP domain proteins [CHIP-seq]

first: Francesco Nicola

last: Carelli

overall_design: 50 single-end ChIP-seq libraries were generated from EGS+formaldehyde fixed nuclei from starved L1 C. elegans strains (wt and mutants).

first: Csenge

last: Gal

first: Francesco

first: Alex

last: Appert

first: Chiara

last: Cerrato

first: Ni

last: Huang

first: Yan

last: Dong

first: Jane

last: Murphy

first: Julie

last: Ahringer


title: N6-methyladenine in DNA antagonizes SATB1 in early development [RNA-seq]

status: Public on Jul 15 2020

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: The recent discovery of N6-methyladenine (N6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism. However, the biological role of N6-mA and the molecular pathways that exert its function remain unclear. Here we show that N6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD). Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures. We show that the presence of N6-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD–SATB1 interactions mediated by N6-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.

overall_design: mRNA with HiSeq sequencing

first: Tao

last: Wu

first: Kaixuan

last: Lin

middle: Z


title: N6-methyladenine in DNA antagonizes SATB1 in early development [MeDIP-seq]

overall_design: DNA immunoprecipitation with HiSeq sequencing


title: N6-methyladenine in DNA antagonizes SATB1 in early development


title: STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

summary: Cohesin exists in two variants, containing either STAG1 or STAG2. STAG2 is one of the most commonly mutated genes in human cancer, and a major bladder cancer tumor suppressor. Little is known about how its inactivation contributes to tumor development. Here, we analyze the genomic distribution of STAG1 and STAG2 and perform STAG2 loss-of-function experiments using RT112 bladder cancer cells; we then analyze the resulting genomic effects by integrating gene expression and chromatin interaction data.

overall_design: One control and two STAG2-silenced conditions were evaluated.

first: Eleonora

last: Lapi

first: Vera

last: Pancaldi

first: Mirabai

last: Cuenca

first: Enrique

last: Carrillo-de-Santa-Pau

first: Miguel

last: Madrid-Mencia

first: Helene

last: Neyret-Kahn

first: François

last: Radvanyi

last: Rodríguez

first: Yasmina

last: Cuartero

last: Serra

first: Dily

last: Francois

first: Alfonso

last: Valencia

first: Marc

last: Marti-Renom

first: Francisco

middle: X

last: Real


title: N6-methyladenine in DNA antagonizes SATB1 in early development [ATAC-seq]

last: Xiao

overall_design: ATAC-seq following Alkbh1 overexpression in embryonic stem cells

last: Wu


title: A modular differentiation system maps multiple human kidney lineages from pluripotent stem cells

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc


title: A modular differentiation system maps multiple human kidney lineages from pluripotent stem cells [scRNA-Seq]

summary: Recent studies using human pluripotent stem cells (hPSCs) have developed protocols to induce kidney-lineage cells and reconstruct kidney organoids. However, the separate generation of metanephric nephron progenitors (NPs), mesonephric NPs and ureteric bud (UB) cells, which constitute embryonic kidneys, in in vitro differentiation culture systems has not been fully investigated. Here we created a culture system in which these mesoderm-like cell types as well as paraxial and lateral plate mesoderm-like cells were separately generated from hPSCs. We succeeded in recapitulating nephrogenic niches from separately induced metanephric NP-like and UB-like cells, which were subsequently differentiated into glomeruli, renal tubules and collecting ducts in vitro and further vascularized in vivo. Our selective differentiation protocols should contribute to understanding the mechanisms underlying human kidney development and diseases and also supply cell sources for regenerative therapies.

overall_design: Two kinds of iPS cell-derived nephron progenitors were generated by different culture conditions.

first: Hiraku

last: Tsujimoto

first: Tomoko

last: Kasahara

first: Shin-ichi

last: Sueta

first: Toshikazu

last: Araoka

first: Satoko

last: Sakamoto

first: Chihiro

last: Okada

first: Kenji

last: Osafune


title: Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

status: Public on Aug 26 2020

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

summary: Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus which has been used as a biocontrol agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. Here, chronically infected beetles were collected from the Philippines, Fiji, PNG and the Solomon Islands (SI). RNAseq was performed to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as gp034, lef-8, lef-4 and vp91. We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes such as gp01, gp022 and gp107 were differentially expressed among different strains. Additionally, small RNA sequencing from SI population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.

overall_design: Adult female Coconut Rhinoceros Beetles (O. rhinoceros) were collected from the Philippines (Los Baños) and three different South Pacific countries, Fiji (Sigatoka, Viti Levu), Papua New Guinea (Kimbe, New Britain) and Solomon Islands (Honiara, Guadalcanal) using traps baited with aggregation pheromone (Oryctalure, P046-Lure, ChemTica Internacional, S. A., Heredia Costa Rica) between June-October 2019. We have 11 OrNV infected beetles in this study.

first: Michael

middle: J

last: Furlong


title: A modular differentiation system maps multiple human kidney lineages from pluripotent stem cells [RNA-Seq]

overall_design: Two kinds of iPS cell-derived nephron progenitors and corresponding organoids were generated by different culture conditions.


title: N6-methyladenine in DNA antagonizes SATB1 in early development [Maternal-fetal interface RNA-seq]

first: Andrew

overall_design: mRNA extraction of maternal-fetal interface with HiSeq sequencing

first: Myles

middle: H

last: Alderman III


title: N6-methyladenine in DNA antagonizes SATB1 in early development [ChIP-seq]

overall_design: Satb1 ChIP-seq following Alkbh1 overexpression in embryonic stem cells

first: Tao

first: Kaixuan

last: Lin


title: GPR35 mediates lysophosphatidic acid-signaling in bone marrow-derived macrophages at the transcriptional level

status: Public on Jun 23 2020

first: DBM Bioinformatics

last: Core Facility

summary:
Purpose: Our previous experiments showed that LPA activated inhibitory G-protein signaling in human GPR35-transfected cells. We wanted to test the LPA signaling in presence or absence of GPR35.
Methods: We isolated RNA from bone-marrow derived macrophages (BMDMs) from WT or GPR35-deficient mice that were treated with LPA or LPS, and left untreated for control.
Results: We have found that GPR35-deficiency alters the transcriptional profiles in response to LPA in BMDMs. On the other hand, LPS-treated WT and GPR35-deficient BMDMs showed similar transcriptional changes.
Conclusion: GPR35-deficientcy alters the LPA but not LPS signaling.

overall_design: mRNA profiles of cont, LPA- or LPS-treated WT or GPR35-deficient BMDMs

first: Berna

last: Kaya

first: Philippe

last: Demoughin

first: Christian

last: Beisel

first: Florian

last: Geier


title: Expression data from sgPPARD and sgCtrl of HCC cells

status: Public on Jun 09 2020

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Hepatocellular carcinoma (HCC) represents the major subtype of liver cancer, characterized with a high rate of recurrence and heterogeneity. Liver cancer stem cells (CSCs) may account for a hierarchical organization of heterogeneous cancer cells. However, how PPARẟ sustain liver CSCs self-renewal remains largely unknown.

overall_design: We used RNA-seq to discover the differential expressed genes underlying sgPPARD and sgCtrl.

first: Jing

first: Xiaoyu

last: Li

first: Xushen

last: Xiong


title: S1-Domain RNA Binding Protein (CvfD) Is a New Post-Transcriptional Regulator That Mediates Cold Shock, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39

status: Public on Jul 01 2020

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

summary: Post-transcriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode in its genome any homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. Instead, the pneumococcal genome contains genes for at least six S1 RNA-binding domain proteins, which includes ribosomal protein S1 (rpsA), polynucleotide phosphorylase (pnpA), RNase R (rnr), and three proteins of unknown function. Here, we characterize the function of one of these conserved, yet uncharacterized S1-domain proteins, SPD_1366, which we have renamed CvfD (Conserved virulence factor D), since loss of this protein results in a attenuation of virulence in a murine pneumonia model. We also report that deletion of cvfD impacts expression of 144 transcripts including the pst1 operon, encoding the phosphate transport system 1 in S. pneumoniae. We further show that CvfD post-transcriptionally regulates the PhoU2 master regulator of the pneumococcal dual phosphate transport system by binding phoU2 mRNA and impacting translation. CvfD not only controls expression of phosphate transporter genes, but also functions as a global regulator impacting cold sensitivity and the expression of sRNAs and genes involved in diverse cellular functions, including manganese uptake and zinc efflux. Together, our data suggest that CvfD exerts a broad impact on pneumococcal physiology and virulence via post-transcriptional gene regulation.

overall_design: Characterization of S1-domain RNA Binding Protein (CvfD) in Streptococcus pneumoniae D39 using RNA-seq. Wildtype S. pneumoniae strain and its derived cvfD mutants were tested in triplicates.